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- PDB-6vvr: Q0 fused 4-OT wild type symmetric trimer -

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Basic information

Entry
Database: PDB / ID: 6vvr
TitleQ0 fused 4-OT wild type symmetric trimer
ComponentsTautomerase
KeywordsISOMERASE / symmetric / fused / 4-oxalocrotonate tautomerase
Function / homologyIsomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / 4-oxalocrotonate tautomerase / Tautomerase enzyme / : / Tautomerase/MIF superfamily / isomerase activity / Tautomerase
Function and homology information
Biological speciesBordetella trematum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMedellin, B.P. / Whitman, C.P. / Zhang, Y.J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-129331 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-41239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
Robert A. Welch FoundationF-1334 United States
Robert A. Welch FoundationF-1778 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.
Authors: Medellin, B.P. / Lancaster, E.B. / Brown, S.D. / Rakhade, S. / Babbitt, P.C. / Whitman, C.P. / Zhang, Y.J.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tautomerase
B: Tautomerase
C: Tautomerase


Theoretical massNumber of molelcules
Total (without water)37,3793
Polymers37,3793
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-33 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.943, 72.943, 82.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Tautomerase


Mass: 12459.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella trematum (bacteria) / Gene: xylH, SAMEA3906487_04185
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A157L8Q0, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium sulfate, 27-33% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→35.84 Å / Num. obs: 39332 / % possible obs: 98.8 % / Redundancy: 5.6 % / CC1/2: 0.996 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3844 / CC1/2: 0.738 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UNQ

5unq


Resolution: 1.8→35.84 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2054 --
Rwork0.1719 --
obs-39332 96.6 %
Displacement parametersBiso max: 65.69 Å2 / Biso mean: 27.4656 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 0 392 2999
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection
Rfree0.2136 -
Rwork0.2127 -
obs-3844

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